The Phosphoglycerate Kinase (Pgk) Gene Family - An Example of Evolution by Gene Duplication
| dc.contributor.advisor | McCarrey, John R. | |
| dc.contributor.author | Trejo, Pedro | |
| dc.contributor.committeeMember | Wang, Yufeng | |
| dc.contributor.committeeMember | Livi, Carolina | |
| dc.contributor.committeeMember | Sunter, Garry | |
| dc.contributor.committeeMember | Cassill, Aaron | |
| dc.date.accessioned | 2024-03-08T16:00:12Z | |
| dc.date.available | 2024-03-08T16:00:12Z | |
| dc.date.issued | 2013 | |
| dc.description | This item is available only to currently enrolled UTSA students, faculty or staff. To download, navigate to Log In in the top right-hand corner of this screen, then select Log in with my UTSA ID. | |
| dc.description.abstract | We have investigated the phosphoglycerate kinase (<italic>Pgk</italic>) gene family to test certain predictions of Susumo Ohno’s theory of Evolution by Gene Duplication. Specifically, we have examined multiple genome databases for evidence that the <italic>Pgk2</italic> retrogene has accumulated DNA sequence changes subsequent to its origin by retroposition that have facilitated the evolution of certain specialized functions in this gene that are distinct from those in the <italic>Pgk1</italic> gene which has retained characteristics and functions similar to the progenitor <italic>Pgk</italic> gene. The specializations investigated in the <italic>Pgk2</italic> gene include potential unique sequences in 1) the promoter region to confer tissue-specific regulation of transcription, 2) the 3’−untranslated region to confer posttranscriptional regulation, and 3) the coding sequence to confer regulation of intracellular localization of the encoded protein. Our bioinformatics analyses using 11 eutherian Pgk genes indicates that at the transcriptional level, the <italic>Pgk1</italic> promoters have conserved a CpG−island whereas the <italic>Pgk2</italic> genes seem to have lost the CpG−island presumably present after retroposition. The metatherian opossum <italic>Pgk1</italic> promoter has conserved a CpG−island. The <italic>Pgk2</italic> promoters in opossum, tammar wallaby, and Tasmanian devil (all metatherian species) also contain CpG−islands of varying strengths. In addition, the eutherian <italic>Pgk1</italic> core promoters have conserved two CAAT−/GC−box pairs and a single NF1−like element, while the <italic>Pgk2</italic> core promoters have conserved a single CAAT−/GC−box pair and gained an E3/E4 enhancer sequence essential for testis−specific expression that appears to have derived from the NF1−like element. The opossum (metatherian) <italic>Pgk1</italic> core promoter has conserved a CAAT−box pair and a single GC−box, while surprisingly, the metatherian (opossum and tammar wallaby) <italic>Pgk2</italic> core promoters lack CAAT− and GC−boxes, and any other standard core promoter elements. At the posttranscriptional level, our results indicate that seven footprints are conserved in eutherian <italic>Pgk1</italic> 3’−UTRs, but these are not generally found in eutherian <italic>Pgk2</italic> 3’−UTRs. <italic>Pgk2</italic> 3’−UTRs have retained only one element also found in <italic>Pgk1</italic> 3’−UTRs, but have gained multiple novel elements not present in <italic>Pgk1</italic> 3’−UTRs, including two putative PTBP2 binding sites important for <italic>Pgk2</italic> mRNA stability. In addition, the opossum <italic>Pgk1</italic> 3’−UTR has conserved three of the seven elements observed in eutherian <italic>Pgk1</italic> 3’−UTRs, and two of these are also observed in the putative Tasmanian devil <italic>Pgk1</italic> 3’−UTR. Unlike the promoter sequences regulating testis−specific transcription of the <italic>Pgk2</italic> gene and the 3’−UTR sequences regulating posttranscriptional delay of the <italic>Pgk2</italic> mRNA, we did not find any specific conserved sequences within the eutherian PGK2 coding region that appear to regulate intracellular localization of the PGK protein. Overall, the eutherian and metatherian comparative studies support the idea that the <italic>Pgk2</italic> promoter and 3’−UTR diverged from <italic>Pgk1</italic>−like sequences by gradually acquiring sequence changes leading to two specialized functions associated with the <italic>Pgk2</italic> gene —testis−specific expression and translational delay, both of which facilitate expression of the PGK2 isozyme in eutherian spermatogenic cells. Therefore, our results are consistent with Ohno’s theory of Evolution by Gene Duplication. | |
| dc.description.department | Integrative Biology | |
| dc.format.extent | 124 pages | |
| dc.format.mimetype | application/pdf | |
| dc.identifier.uri | https://hdl.handle.net/20.500.12588/5963 | |
| dc.language | en | |
| dc.subject | duplication | |
| dc.subject | localization | |
| dc.subject | Pgk | |
| dc.subject | Phosphoglycerate | |
| dc.subject | posttranscription | |
| dc.subject | transcription | |
| dc.subject.classification | Evolution & development | |
| dc.subject.classification | Molecular biology | |
| dc.subject.classification | Bioinformatics | |
| dc.title | The Phosphoglycerate Kinase (Pgk) Gene Family - An Example of Evolution by Gene Duplication | |
| dc.type | Thesis | |
| dc.type.dcmi | Text | |
| dcterms.accessRights | pq_closed | |
| thesis.degree.department | Integrative Biology | |
| thesis.degree.grantor | University of Texas at San Antonio | |
| thesis.degree.level | Doctoral | |
| thesis.degree.name | Doctor of Philosophy |
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